Piperonyl butoxide (PBO) is a pesticide synergist with widespread use and human exposure that was discovered to inhibit Sonic hedgehog (Shh) signaling, a pathway required for numerous developmental processes. Previous examinations of PBO’s potential for developmental toxicity have generated seemingly conflicting results. We investigated the impact of acute PBO exposure targeting Shh pathway activity during palate and limb morphogenesis. Timed-pregnant C57BL/6 J mice were exposed to a single PBO dose (67–1800 mg/kg) at gestational day (GD) 9.75, and litters were collected at GD10.25 and GD10.75 to examine Shh pathway activity or GD17 for phenotypic assessment. PBO exposure induced dose-dependent limb malformations and cleft palate in the highest dose group. Following PBO exposure, reduced expression of the Shh pathway activity markers Gli1 and Ptch1 was observed in the embryonic limb buds and craniofacial processes. These findings provide additional evidence that prenatal PBO exposure targeting Shh pathway activity can result in malformations in mice that parallel common etiologically complex human birth defects.